Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

A Whole Genome Association Study on Meat Quality Traits Using High Density SNP Chips in a Cross between Korean Native Pig and Landrace

  • Lee, K.T. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science) ;
  • Lee, Y.M. (School of Biotechnology, Yeungnam University) ;
  • Alam, M. (School of Biotechnology, Yeungnam University) ;
  • Choi, B.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science) ;
  • Park, M.R. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science) ;
  • Kim, K.S. (Department of Animal Science, Chungbuk National University) ;
  • Kim, T.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science) ;
  • Kim, Jong-Joo (School of Biotechnology, Yeungnam University)
  • Received : 2012.09.04
  • Accepted : 2012.09.27
  • Published : 2012.11.01
Download PDF
⟨ Previous Next ⟩

Abstract

A whole genome association (WGA) study was performed to detect significant polymorphisms for meat quality traits in an $F_2$ cross population (N = 478) that were generated with Korean native pig sires and Landrace dams in National Livestock Research Institute, Songwhan, Korea. The animals were genotyped using Illumina porcine 60k SNP beadchips, in which a set of 46,865 SNPs were available for the WGA analyses on ten carcass quality traits; live weight, crude protein, crude lipids, crude ash, water holding capacity, drip loss, shear force, CIE L, CIE a and CIE b. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model, after adjusting for sex, sire and slaughter stage as fixed effects. With the significant SNPs for each trait (p<0.001), a stepwise regression procedure was applied to determine the best set of SNPs with the additive and/or dominance effects. A total of 106 SNPs, or quantitative trait loci (QTL) were detected, and about 32 to 66% of the total phenotypic variation was explained by the significant SNPs for each trait. The QTL were identified in most porcine chromosomes (SSCs), in which majority of the QTL were detected in SSCs 1, 2, 12, 13, 14 and 16. Several QTL clusters were identified on SSCs 12, 16 and 17, and a cluster of QTL influencing crude protein, crude lipid, drip loss, shear force, CIE a and CIE b were located between 20 and 29 Mb of SSC12. A pleiotropic QTL for drip loss, CIE L and CIE b was also detected on SSC16. These QTL need to be validated in commercial pig populations for genetic improvement in meat quality via marker-assisted selection.

Keywords

References

  1. Andersson, L., C. S. Haley, H. Ellegren, S. A. Knott, M. Johansson, K. Andersson, L. Andersson-Eklund, I. Edfors-Lilja, M. Fredholm, I. Hansson, J. Hakansson and K. Lundström. 1994. Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263:1771-1774. https://doi.org/10.1126/science.8134840
  2. Andersson-Eklund, L., L. Marklund, K. Lundstrom, C. S. Haley, K. Andersson, I. Hansson, M. Moller and L. Andersson. 1998. Mapping quantitative trait loci for carcass and meat traits in a Wild boar${\times}$Large White intercross. J. Anim. Sci. 76:694-700.
  3. Choi, B. H., Y.-M. Lee, M. Alam, J.-H. Lee, T.-H. Kim, K.-S. Kim and J. -J. Kim. 2011. Detection of Mendelian and parent-oforigin quantitative trait loci for meat quality in a cross between Korean native pig and Landrace. Asian-Aust. J. Anim. Sci. 24:1644-1650. https://doi.org/10.5713/ajas.2011.11166
  4. Bidanel, J. P. and M. Rothschild. 2002. Current status of quantitative trait locus mapping in pigs. Pig News and Information 23:39N-53N.
  5. Bidanel, J. P., D. Milan, N. Iannuccelli, Y. Amigues, M. Y. Boscher, F. Bourgeois, C. J. Caritez, J. Gruand, P. L. Roy, H. Lagant, R. Quintanilla, C. Renard, J. Gellin, L. Ollivier and C. Chevalet. 2001. Detection of quantitative trait loci for growth and fatness in pigs. Genet. Sel. Evol. 33:289-309. https://doi.org/10.1186/1297-9686-33-3-289
  6. Ovilo, C., A. Clop, J. L. Noguera, M. A. Oliver, C. Barragan, C. Rodriguez, L. Silio, M. A. Toro, A. Coll, J. M. Folch, A. Sanchez, D. Babot, L. Varona and M. Pérez-Enciso 2002. Quantitative trait locus mapping for meat quality traits in an Iberian${\times}$Landrace F2 pig population. J. Anim. Sci. 80:2801-2808.
  7. Cho, S.-H. 2006. Characteristics of carcass and meat qualities in Korean native pigs. In symposium of conservation and utilization of Korean native pigs. Korean Livestock Research Institute, p. 33-50.
  8. Choy, Y. H., G. J. Jeon, T. K. Kim, B. H. Choi and H. W. Chung. 2002a. Ear type and coat color on growth performances of crossbred pigs. Asian-Aust. J. Anim. Sci. 15:1178-1181. https://doi.org/10.5713/ajas.2002.1178
  9. Choy, Y. H., G. J. Jeon, T. K. Kim, B. H. Choi, I. C. Cheong, H. K. Lee, K. S. Seo, S. D. Kim, Y. I. Park and H. W. Chung. 2002b. Genetic analyses of carcass characteristics in crossbred pigs: cross between Landrace sows and Korean wild boars. Asian-Aust. J. Anim. Sci. 15:1080-1084. https://doi.org/10.5713/ajas.2002.1080
  10. Clop, A., C. Ovilo, M. Perez-Enciso, A. Cercos, A. Tomas, A. Fernandez, A. Coll, J. M. Folch, C. Barragan, I. Diaz, M. A. Oliver, L. Varona, L. Silio, A. Sanchez and J. L. Noguera. 2003. Detection of QTL affecting fatty acid composition in the pig. Mamm. Genome. 14:650-656. https://doi.org/10.1007/s00335-002-2210-7
  11. De Koning, D. J., L. L. G. Janss, A. P. Rattink, P. A. van Oers, B. J. de Vries, M. A. M. Groenen, J. J. der Poel, P. N. de Groot, E. W. Brascamp and J. A. M. van Arendonk. 1999. Detection of quantitative trait loci for back fat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics 152:1679-1690.
  12. De Koning, D., B. Harlizius, A. P. Rattink, M. A. M. Groenen, E. W. Brascamp and J. A. M. van Arendonk. 2001. Detection and characterization of quantitative trait loci for meat quality traits in pigs. J. Anim. Sci. 79:2812-2819.
  13. Duthie, C., G. Simm, A. Doeschl-Wilson, E. Kalm, P. W. Knap and R. Roehe. 2008. Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake. Anim. Genet. 39:130-140. https://doi.org/10.1111/j.1365-2052.2007.01689.x
  14. Fan, B., S. K. Onteru, D. Garrick, K. J. Stalder and M. F. Rothschild. 2009. A genome-wide association study for pig production and feet and leg structure traits using the PorcineSNP60 BeadChip. Pig Genome III Conference, November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 6.
  15. Gorbach, D. M., W. J. Cai, C. M. Dekkers, J. M. Young and D. J. Garrick. 2009. Whole-genome analyses for genes associated with residual feed intake and related traits utilizing the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4. Hinxton, UK. Abstract No. 11.
  16. Hu, Z. L., E. R. Fritz and J. M. Reecy. 2007. AnimalQTLdb: A livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res. 35:D604-D609. https://doi.org/10.1093/nar/gkl946
  17. Hwang, I. H., B. Y. Park, S. H. Cho, J. H. Kim and J. M. Lee. 2004. Identification of muscle proteins related to objective meat quality in Korean native black pig. Asian-Aust. J. Anim. Sci. 17:1599-1607. https://doi.org/10.5713/ajas.2004.1599
  18. Janss, L. L. G., A. M. Johan, J. A. M. van Arendonk and E. W. Brascamp. 1997. Segregation analyses for presence of major genes affecting growth, backfat, and litter size in Dutch Meishan crossbreds. J. Anim. Sci. 75:2864-2876.
  19. Jennen, D. G. J., A. D. Brings, G. Liu, H. Jüngst, E. Tholen, E. Jonas, D. Tesfaye, K. Schellander and C. Phatsara. 2007. Genetic aspects concerning drip loss and water-holding capacity of porcine meat. J. Anim. Breed. Genet. 124(Suppl. 1):2-11. https://doi.org/10.1111/j.1439-0388.2007.00681.x
  20. Kim, E. H., B. H. Choi, K. S. Kim, C. K. Lee, B. W. Cho, T. H. Kim and J. J. Kim. 2007. Detection of Mendelian and parent-of-origin quantitative trait loci in a cross between Korean native pig and Landrace I. growth and body composition traits. Asian-Aust. J. Anim. Sci. 20:669-676. https://doi.org/10.5713/ajas.2007.669
  21. Kim, T. H., K. S. Kim, B. H. Choi, D. H. Yoon, G. W. Jang, K. T. Lee, H. Y. Chung, H. Y. Lee, H. S. Park and J. W. Lee. 2005. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J. Anim. Sci. 83:2255-2263.
  22. Knott, S. A., L. Marklund, C. S. Haley, K. Andersson, W. Davies, H. Ellegren, M. Fredholm, I. Hansson, B. Hoyheim, K. Lundstrom, M. Moller and L. Andersson. 1998. Multiple markers mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 149:1069-1080.
  23. Li, H. D., M. S. Lund, O. F. Christensen, V. R. Gregersen, P. Henckel and C. Bendixen. 2010. Quantitative trait loci analysis of swine meat quality traits. J. Anim. Sci. 88:2904-2912. https://doi.org/10.2527/jas.2009-2590
  24. Li, X., S. -W. Kim, K. -T. Do, Y. -K. Ha, Y. -M. Lee, S. -H. Yoon, H. -B. Kim, J. -J. Kim, B. -H. Choi and K. -S. Kim. 2011. Analyses of porcine public SNPs in coding-gene regions by resequencing and phenotypic association studies. Mol. Biol. Rep. 38:3805-3820. https://doi.org/10.1007/s11033-010-0496-1
  25. Liu, G., D. G. J. Jennen, E. Tholen, H. Juengst, T. Kleinwächter, M. Hölker, D. Tesfaye, G. Ün, H. -J. Schreinemachers, E. Murani, S. Ponsuksili, J.-J. Kim, K. Schellander and K. Wimmers. 2007. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Anim. Genet. 38:241-252. https://doi.org/10.1111/j.1365-2052.2007.01592.x
  26. Ma, J., J. Ren, Y. Guo, Y. Duan, N. Ding, L. Zhou, L. Li, X. Yan, K. Yang, L. Huang, Y. Song, J. Xie, D. Milan and L. Huang. 2009. Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc${\times}$Chinese Erhualian resource population. Anim. Genet. 40:637-647. https://doi.org/10.1111/j.1365-2052.2009.01892.x
  27. Malek, M., J. C. M. Dekkers, H. K. Lee, T. Baas and M. F. Rothschild. 2001a. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mamm. Genome 12: 630-636. https://doi.org/10.1007/s003350020018
  28. Malek, M., J. C. M. Dekkers, H. K. Lee, T. J. Baas, K. Prusa, E. Huff-Lonergan and M. F. Rothschild. 2001b. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mamm. Genome 12:637-645. https://doi.org/10.1007/s003350020019
  29. Markljung, E., M. H. Braunschweig, P. Karlskov-Mortensen, C. S. Bruun, M. Sawera, I.-C. Cho, I. Hedebro- Velander, Å. Josell, K. Lundström, G. von Seth, C. B. Jørgensen, M. Fredholm and L. Andersson. 2008. Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II: Meat quality traits. BMC Genet. 9:22
  30. Munoz, G., E. Alves, A. Fernandez, C. Ovilo, C. Barragan, J. Estelle, R. Quintanilla, J. M. Folch, L. Silio, M. C. Rodriguez and A. I. Fernandez. 2007. QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes. Anim. Genet. 38:639-646. https://doi.org/10.1111/j.1365-2052.2007.01668.x
  31. Murani, E., M. F. W. te Pas, K. C. Chang, R. Davoli, J. W. M. Merks, H. Henne, R. Wörner, H. Eping, S. Ponsuksili, K. Schellander, N. da Costa, D. Prins, B. Harlizius, E. Knol, M. Cagnazzo, S. Braglia and K. Wimmers. 2005. Analysis of effects of genes differentially expressed during myogenesis on pork quality. 56th Annual Meeting of the European Association for Animal Production. June 5-8, Uppsala, Sweden (Abstr)
  32. Neter, J., W. Wasserman and M. H. Kutner. 1990. Applied linear statistical models. 3rd ed. Irwin. Boston.
  33. Onteru, S. K., B. Fan, D. Garrick, K. J. Stalder and M. F. Rothschild. 2009. Whole genome analyses for pig reproductive traits using the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 5.
  34. Paszek, A. A., P. J. Wilkie, G. H. Flickinger, G. A. Rohrer, L. J. Alexander, C. W. Beattie and L. B. Schook. 1999. Interval mapping of growth in divergent swine cross. Mamm. Genome 10:117-122. https://doi.org/10.1007/s003359900955
  35. Ramos, A. M., J. W. M. Bastiaansen, G. S. Plastow and M. F. Rothschild. 2009. Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations. Anim. Genet. 40:774-778. https://doi.org/10.1111/j.1365-2052.2009.01907.x
  36. Rohrer, G. A. 2000. Identification of quantitative trait loci affecting birth characters and accumulation of back fat and weight in Meishan-White Composit resource population. J. Anim. Sci. 78:2547-2553.
  37. Rohrer, G. A. and J. Keele. 1998. Identification of quantitative trait loci affecting carcass composition in swine II. Muscling and wholesale product trait yield traits. J. Anim. Sci. 76:2255-2262.
  38. Rothschild, M. F., H. C. Liu, C. K. Tuggle, T. P. Yu and L. Wang. 1995. Analysis of chromosome 7 genetic markers for growth and carcass performance traits. J. Anim. Breed. Genet. 112: 341-348. https://doi.org/10.1111/j.1439-0388.1995.tb00576.x
  39. Rothschild, M. F., Z. Hu and Z. Jiang. 2007. Advances in QTL mapping in pigs. Int. J. Biol. Sci. 3:192-197.
  40. Sanchez, M. -P., N. Iannuccelli, B. Basso, J.- P. Bidanel, Y. Billon, G. Gandemer, H. Gilbert, C. Larzul1, C. Legault, J. Riquet, D. Milan and P. L. Roy. 2007. Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc${\times}$Large White cross. BMC Genet. 8:55.
  41. Soma, Y., Y. Uemoto, S. Sato, T. Shibata, H. Kadowaki, E. Kobayashi and K. Suzuki. 2011. Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population. J. Anim. Sci. 89:601-608. https://doi.org/10.2527/jas.2010-3119
  42. Stearns, T. M., J. E. Beever, B. R. Southey, M. Ellis, F. K. McKeith and S. L. Rodriguez-Zas. 2005. Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. I. Univariate outbred F2 and sib-pair analyses. J. Anim. Sci. 83:1481-1493.
  43. Thomsen, H., H. K. Lee, M. F. Rothschild, M. Malek and J. C. M. Dekkers. 2004. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. J. Anim. Sci. 82:2213-2228.
  44. Uemoto, Y., Y. Nagamine, E. Kobayashi, S. Sato, T. Tayama, Y. Suda, T. Shibata and K. Suzuki. 2008. Quantitative trait loci analysis on Sus scrofa chromosome 7 for meat production, meat quality, and carcass traits within a Duroc purebred population. J. Anim. Sci. 86:2833-2839. https://doi.org/10.2527/jas.2007-0293
  45. Van Wijk, H. J., B. Dibbits, E. E. Baron, A. D. Brings, B. Harlizius, M. A. M. Groenen, E. F. Knol and H. Bovenhuis. 2006. Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross. J. Anim. Sci. 84:789-799.
  46. Wada, Y., T. Akita, T. Awata, T. Furukawa, N. Sugai, Y. Inage, K. Ishii, Y. Ito, E. Kobayashi, H. Kusumoto, T. Matsumoto, S. Mikawa, M. Miyake, A. Murase, S. Shimanuki, T. Sugiyama, Y. Uchida, S. Yanai and H. Yasue. 2000. Quantitative trait loci (QTL) analysis in a Meishan${\times}$Gottingen cross population. Anim. Genet. 31:376-384. https://doi.org/10.1046/j.1365-2052.2000.00696.x

Cited by

  1. Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs vol.26, pp.3-4, 2015, https://doi.org/10.1007/s00335-015-9558-y
  2. Establishment and identification of cell lines from type O blood Korean native pigs and their efficiency in supporting embryonic development via somatic cell nuclear transfer vol.19, pp.4, 2018, https://doi.org/10.4142/jvs.2018.19.4.492
  3. Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs vol.47, pp.1, 2015, https://doi.org/10.1186/s12711-014-0080-6